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GBrowse PAG 2009 Workshop

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PAG 2009 The Generic Genome Browser: A Hands on Workshop for Installing, Configuring and Using Your Own GBrowse

January 11, 2009
Plant and Animal Genome Conference
San Diego, California, USA


This page provides additional information about the GBrowse workshop at the Plant and Animal Genome XVII Conference (PAG 2009) held in San Diego on January 10-14, 2009. This workshop was attended by over 60 people.

Note on Installation

An installer package for Microsoft Windows can be downloaded here.

  • download the zip file and double-click to unpack
  • enter the directory 'a' and double-click the executable file 'install_gbrowse'
  • This will install Perl, Apache Web server, and other requirements to run GBrowse on your system

Also, see the Windows installation guide and guides for other operating systems.

Overview

This was be a hands-on tutorial on how to install and use the GBrowse genome browser.

Tutorial Level

Beginner to Intermediate. Students should be comfortable performing simple system administration tasks like stopping and starting services.

Students who wish to use their own computer should preinstall the prerequisites described in the GBrowse installation notes, including Perl, Apache, MySQL and (for Unix) BioPerl.

Intended Audience

GBrowse is sufficiently easy to install that a biologist can easily set up and configure a GBrowse server after the initial hurdles of learning about configuration options and file formats are overcome. This class is intended to help them over those hurdles.

Outline

  • The Basics
  • The Data File
  • Defining Tracks
  • Searching for Named Features
  • Adding Descriptions to a Feature
  • Showing multi-segmented features
  • Using Aggregators
  • Showing Protein Coding Genes
  • Showing the Reading Frame
  • Creating Custom Aggregators
  • Showing Quantitative Data
  • Displaying DNA and 3-frame translations
  • Features added in latest release, including draggable and collapsible tracks, and popup balloons

Workshop Instructor

Datasets

Example datasets will be posted prior to the conference.

Other GMOD Presentations and Meetings

GMOD will have a strong presence at PAG 2009, including a workshop on GBrowse_syn, a synteny viewer built on GBrowse. See the list of GMOD related PAG 2009 presentations for more. The January 2009 GMOD Meeting was held in San Diego, immediately after PAG 2009.